The SD card should have at least one partition formatted to FAT (FAT16 or FAT32). Unzip the genplus-gx.zip folder, in it you should find a folder named "apps". Move the "apps" folder to the root of your SD Card. If your Wii is correctly softmodded it should now be able to run the emulator through The Homebrew Channel. Make a folder in your SD Card root called "genplus" place the "genplus_wii.dol" file in the folder, make a new folder called "roms" in the "genplus" folder. The emulator will automatically look for roms in genplus/roms folder.
The USB drive should have at least one partition formatted to FAT (FAT16 or FAT32), other file systems (NTFS, EXT2, etc) are not supported. If no SD card is inserted when the emulator starts, it automatically creates a directory named “/genplus” at the root of your USB drive partition, as well as a few subdirectories, all required by the emulator to store important files (configuration, cheat files, SRAM files, screenshots, etc). By default, the emulator will look for ROM files in the /genplus/roms directory but you can place them anywhere you want, the menu keeping trace of the last accessed directory for each device. To use an USB2 drive, you must have IOS58 installed (it should be automatically installed with System Menu 4.3 update). You should also load the emulator through the Homebrew Channel, using the provided meta.xml file and make sure Homebrew Channel is using IOS58 as default IOS. (copied from the README included with the emulator)
Mega CD emulation
Original BIOS ROM files are required: unzip & rename them to bios_CD_U.bin, bios_CD_E.bin, bios_CD_J.bin in /genplus/bios/ directory
Audio tracks (CD-DA) are not supported yet